RetrogeneDB ID: retro_mdom_685

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:95140307..95140673(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSMODG00000019428
• Aliases: None
• Description: zinc finger, AN1-type domain 6 [Source:HGNC Symbol;Acc:30164]

Sequence

>retro_mdom_685
ATGGCTCAAGAAACTAACCATAGCCAAGTGCCTATGCTTTGTTCCACTGGCTGTGGATTTTATGGAAACCCTCGTACAAA
TGGCATGTGTTCAGTATGTTATAAAGAACATCTTCAAAGACAGAATAGTAGTAATGGTAGAATTAGCCCACCTGCAACTT
CTGTCAGTAGTCTGTCTGAATCTTTACCAGTTCAGTGCACAAATGGCAATGTCCCAGAAGCTCAGTCAACATTAGACTCC
ACGTTTTCCCCATCTATGCAGCCAAGTCCTGTATCAAATCAATCACTTTTATCAGACTCTGTAGCATCTACCCAAATGGA
AAGTACATCTGTGGACAAAGCAGTACCTGAAACAGACGATCTGCAA

Alignment

ORF - retro_mdom_685 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.72 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQNSSNGRISPPATSVSSLSESLPVQCTDDN
          MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQNSSNGRISPPATSVSSLSESLPVQCT..N
Retrocopy MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQNSSNGRISPPATSVSSLSESLPVQCTNGN

Parental  VPEAQSTLDSTSSPSMQPSPVSNQSLLSDSVASTQVESTSVDKAVPETDDLQ
          VPEAQSTLDST.SPSMQPSPVSNQSLLSDSVASTQ.ESTSVDKAVPETDDLQ
Retrocopy VPEAQSTLDSTFSPSMQPSPVSNQSLLSDSVASTQMESTSVDKAVPETDDLQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	184.99 RPM
SRP007412_cerebellum	0.00 RPM	157.02 RPM
SRP007412_heart	0.00 RPM	169.65 RPM
SRP007412_kidney	0.00 RPM	331.84 RPM
SRP007412_liver	0.00 RPM	363.02 RPM
SRP007412_testis	0.00 RPM	297.60 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_685 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_685 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685 ,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,